Research workbench
Crystal structures of cyanuric acid hydrolase from moorella thermoacetica complexed with cyanuric acid
Analyse Crystal structures of cyanuric acid hydrolase from moorella thermoacetica… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6BUP
- Type
- protein
- Length
- 1,449 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cyanuric acid amidohydrolase
- EC
- 3.5.2.15
- UniProt
- Q2RGM7
- Ligands
- WDL, CA, CL
- Pockets
- 8 · best druggability 0.83
Structure
x-ray diffraction · 3 distinct chains · 35% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cyanuric acid amidohydrolase (EC 3.5.2.15) | protein | 361 | 36% helix, 27% strand | Q2RGM7 |
| B, C | Cyanuric acid amidohydrolase (EC 3.5.2.15) | protein | 363 | 35% helix, 27% strand | Q2RGM7 |
| D | Cyanuric acid amidohydrolase (EC 3.5.2.15) | protein | 362 | 35% helix, 26% strand | Q2RGM7 |
Ligands and binding sites
- WDL · 1,3,5-triazine-2,4,6-triol · ligand · 3 copies · chains B, C
- CA · Calcium ion · metal · 4 copies · chains A, B, C, D
- CL · Chloride ion · ion · 3 copies · chains B, D
- PDO · 1,3-propandiol · additive · 11 copies · chains A, C, B
- MLI · Malonate ion · additive · 4 copies · chains A, B, C, D
- PEG · Di(hydroxyethyl)ether · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1168 | 0.83 | 0.84 | 118 | PDO, WDL |
| 2 | 1167 | 0.82 | 0.83 | 110 | PDO, PEG, MLI, CL |
| 3 | 61 | 0.70 | 0.97 | 18 | empty |
| 4 | 63 | 0.69 | 0.96 | 19 | empty |
| 5 | 381 | 0.62 | 0.77 | 43 | empty |
Interfaces
6 interfaces between chains.
- B–D · 1494 Ų buried · 19 hydrogen bonds · protein-protein
- A–C · 1462 Ų buried · 20 hydrogen bonds · protein-protein
- B–C · 833 Ų buried · 16 hydrogen bonds · protein-protein
- A–D · 683 Ų buried · 14 hydrogen bonds · protein-protein
- C–D · 642 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 6BUP · Crystal structures of cyanuric acid hydrolase from Moorella thermoacetica complexed with… · the same entry in another collection · chain D against D, TM-score 1.00
- Q2RGM7 · AlphaFold monomer V2.0 prediction for cyanuric acid amidohydrolase (Q2RGM7) · a predicted model of the same protein · chain B against A, TM-score 0.99
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt Q2RGM7
- Elsewhere: RCSB PDB 6BUP · PDBe 6BUP · UniProt Q2RGM7
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